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2007 ; 23
(15
): 2018-20
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StrBioLib: a Java library for development of custom computational structural
biology applications
#MMPMID17537750
Chandonia JM
Bioinformatics
2007[Aug]; 23
(15
): 2018-20
PMID17537750
show ga
SUMMARY: StrBioLib is a library of Java classes useful for developing software
for computational structural biology research. StrBioLib contains classes to
represent and manipulate protein structures, biopolymer sequences, sets of
biopolymer sequences, and alignments between biopolymers based on either sequence
or structure. Interfaces are provided to interact with commonly used
bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3,
and tools are provided to read and write many file formats used to represent
bioinformatic data. The library includes a general-purpose neural network object
with multiple training algorithms, the Hooke and Jeeves non-linear optimization
algorithm, and tools for efficient C-style string parsing and formatting.
StrBioLib is the basis for the Pred2ary secondary structure prediction program,
is used to build the astral compendium for sequence and structure analysis, and
has been extensively tested through use in many smaller projects. Examples and
documentation are available at the site below. AVAILABILITY: StrBioLib may be
obtained under the terms of the GNU LGPL license from
http://strbio.sourceforge.net/